Beta Site
by Caroline ONeill
Summary: Sam and Jack are having personal problems and it brings changes to the SGC. Every one is trying to help but they don't want their help.
1. Yellow Envelopes

_Disclaimer: I don't own SG1 and never will._

_Author Notes: Please review- this is my first fan fiction. _

_Summary: Sam and Jack are having a bad time. Set season 7-8 but Janet is still alive so you could call it a AU Fic._

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SG1 sitting in the commissary having an early breakfast as they were leaving for a mission at 1300 hours. General chatting about what they did on there week off after that horrible mission to PX 745897. It had been the final straw they had a run of bad luck four missions in a row. PX745897 wasn't bad as in Jaffa or a Goa'uld fight but it was one of the worst for mud, rain. It was fine and sunny when they arrived it was almost tropical weather. The ruins were a day hike from the gate which gave them one day there and a day to hike back. It wasn't flat; they hiked over a range which what was the delay to the ruins. When they got to the ruins after setting up camp for there two nights stay, the clouds started coming over and it had turned into a thunder storm which lasted the whole two nights.

Daniel got to study the ruins and found nothing of great interest; Carter got all her samples together and helped Daniel with the survey of the building. On the day of there departure they all had had enough of the rain, it had soaked through. Everything was damp and cold so no one was a happy camper. On the way back, Daniel was especially not happy as he had taken a fall on the range and hurt his leg. It wasn't broken but very badly busied and couldn't put any weight on the leg. So Teal'c and O'Neill helped Daniel while Carter had to take most of Daniels pack so it wasn't as heavy.

"So Daniel, hows the leg?" Jack inquired with a smirk written across his face. Continuing "How long Doc keep you in for?" Jack had a quite week keeping to himself doing some personal paper work and maintenance on his house. Jack knew Teal'c had been off-world visiting Ryac so there was nothing interesting there to inquire about and Carter had been in her Lab all week running some test on the doohickie that SG9 brought back from there latest mission. Before Daniel could answer, the loud speakers came to life requesting "Colonel O'Neill, Major Carter to the General Hammond office immediately" blasted over the Base it repeated the words two more times when it finally stoped. Jack looked at his 2IC wondering what the General is wanting, it had to be important to call both of them to his office. Sam stood up saying aloud "What did we do now?"

Walking in silence to the elevators to take them to Level 27 General Hammond's office, each in there own thoughts. They had not spoken much to one another, other than Jack giving her orders or Sam saying "Yes Sir" "No Sir" since they had spent the night together three weeks earlier. It had helped that they were on downtime for a week of that time, but two weeks of not talking and everyone had notice. As they walked the looks the SF's were giving them was making both very uncomfortable and the tension was unbearable.

Reaching the Generals office Jack tapped on the door waiting for a response. Hammond sighed he didn't want to do this but he had no choice these were his top 2 officers and at this stage it was looking at a Court Martial for both of them! He wanted answers to why they had crossed that line!

"Come in Colonel, Major please take a seat!"

"Today's mission has been postponed for now Colonel!"

"Sir what's going on? Why are we not going?" Sam asked having had enough tension between her and Jack but now it was just ridiculous. Seeing the look on the General's face Sam asked "General?"

Hammond slid the photos across the table as he sat down in his chair. Jack picked up the envelope and opened it to pull out 5 by 8 photos of them together at her house. He passed the photos to Sam. She had seen the look on his face and was giving him a, what's going on, I want to know now expression. She looked at the first it was of her and Jack on her porch in a passionate embrace. The second was of them inside her house, Jack didn't have his shirt on and Sam's was in the process of losing hers, then the third photo it was taken from outside her bedroom window, it displayed them naked sleeping while holding tightly to each other. She put them down and faced the General to see what his expression was. He was angry you could tell. But more importantly he was disappointed in them for letting this happen.

They explained what had happen with the alien virus and that Janet knew and had proof that they were both infected but it still didn't excuse them totally.

Hammond wasn't happy that Doctor Frasier new about this and the fact that she didn't inform him of the incident, but could under stand why they went to her as they were protected by Doctor / Patient privilege.

After 3 hours talking to Major Carter, Colonel O'Neill, Doctor Frasier, Joint Chefs and The President it had come to this final decision!

"Ok people this is what we came up with there will be no Court Martials for either of you but Major Cater you are being taken off SG1 and placed on SG9 for the time been. It may be permanent Major I don't know yet! Holding up his hands to stop any interruption. "Dismissed!" After saying that, General Hammond left the room with feeling like the bad guy. These were his two best officers and he just had to hope, this will bring them together not tear them apart.

Sam pushed the chair back and started to walk out the door having tears in her eyes she didn't want to see anyone. Jack doing the same but heading off in the other direction, as he tried to control his anger about the whole situation.

Sam and Jack avoided everyone for the next 7 days. Sam hid in her Lab working in solitude, annoyed at anyone who tried to enter and making sure they new it to. Daniel and Teal'c avoided her; even Janet tried once but got abused for her effort.

Jack was pretty much the same but a lot more vocal and at anyone who walked past.

After 7 days Jack had enough and went to talk to Sam in her Lab, seeing that she had been crying he went to put his arm around her and in a low tone trying to comfort her said "It's going to be ok!" She pushed him away clearly annoyed with him replied

"You're not the one this is affecting I got moved to SG9 Pete called off the engagement every one is looking at me like….." Sam stated to babbling so angry that Jack had said it's going to be ok. He wasn't moved from the team he got off with a bit of yelling from Hammond.

"Wait! Pete called off the engagement. Why?" Jack butted in on her babbling.

Sam replied "They sent the photos to him."

Looking down at her feet she felt like hiding in a dark room her heart was hurting she loved the man in front of her but engaged to another which she loved as well but it was different. Pete could give her a normal life the one she had been craving for a long time and the time on Prometheus had made her realise maybe Sam and Jack will never be and hiding behind the her work wasn't working. Sam didn't mean to fall for Pete but it had happen. She didn't mean to hurt Jack but Pete made her happy and she needed to be happy out side of work. Suddenly Jack spoke breaking her thoughts.

Oh! Sorry! Not really knowing what to say they had both been shown the photos and he knew how he felt but he wasn't the one engaged to her and a photo of her Pete's Fiancée in bed with her CO would not have gone down well. He felt sorry for her she seemed to be the one getting all the consequences of there actions. He was sorry that it had happen the way it did but not sorry that it had happen. It was obvious that she wasn't feeling the same as him. Maybe he had been deluding himself that she still had feelings for him all these years maybe she no longer loved him or maybe she never. Feeling himself getting angry not at her but at himself for ever believing the feelings where mutual.

Feeling like she was about to cry Sam muted "I wish this never happened it was a mistake!" looking at him for a moment before turning and walking away with tears running down her cheeks. Not really knowing where she was going she just walked looking down not even noticing any of the SF standing at the elevator. Sam seemed to be heading for the infirmary.

Janet looked up to see who walked into her Infirmary hoping everything was ok no one hurt, she was shocked to see Sam in tears looking very lost and sad. Janet walked up to Sam and put her arms around her to try and calm her best friend down.

Being that Sam had been hiding in her Lab for the past week not talking to anyone. Now all she wanted to do was go home get a bottle of wine and have a nice long girl talk with Janet. After what had happened in the last week and with Pete she needed to do this, or she was not going to have any friends left.

"Janet can we get out of here? Go to my place and talk, drink wine, get drunk not in that order mind you!" Sam managed to say with a small smile on her face.

"Sure my shift finished 3 hours ago let me just get my stuff, meet you at the elevators!" Janet was happy that Sam had decided to finally talk she would feel better just getting it out into the open.

After leaving the mountain Sam stoped off at the bottle shop while Janet got Chinese from there favourite place. Janet pulled up behind Sam's car grabbing all the food and headed inside ready for a long girl talk. Sam already had a glass of wine in her hand and another on the kitchen table for Janet. Sam stated "Food first then talk while we drink" agreeing Janet placed the food down on the table and served it. Sam had eaten most of her food when she looked up and told her story of last night.

"Pete got here for a week visit, he has been working really hard on this new case and has been in Denver for 3 months now, and he had only been able to come here 2 weekends out of that time."

Janet realising that her and Sam really haven't been talking for months because she didn't even know Pete was away.

"He was opening his mail from Denver when I sore he was opening an envelope.

It looked like the same one General Hammond received with the photos in it."

Janet gasps "No?" "Obviously he sore them."

Nodding her head and looking away Sam slowly replied "Yeap"

About to cry again Sam got up and walked into the Lounge with Janet following her.

Sitting on the couch Sam let the tears fall as she kept talking "We had a big fight. I tried to explain about the virus but he just said that if I loved him enough I would have not slept with the Colonel. He called off the wedding! I loved him Janet I truly do. I don't know why I slept with Jack it just happened. I regret ever sleeping with him!"

Janet just letting her get all of this off her chest but the last comment wasn't true and she knew it. "You don't mean that Sam, you have loved Jack a lot longer than Pete. You and Jack have this connection that can't be broken."

"I should have been stronger and resisted I made a commitment to Pete and I broke it." Breaking for a moment "The Colonel came and sore me today he tried to help and only made it worse. I told him that I regretted that night."

"Sam it will work out he knows you didn't mean it.!"

"Janet! I did mean it! That's the point! I did!" Tears flowing full force now Sam couldn't talk any more, just putting her head down listening to Janet.

"Oh honey" noticing how tired Sam really was Janet grab a blanket and let her cry herself to sleep.

Two hours later Janet walked in to the Lounge and woke Sam up saying she had to have a shower and some more to eat. After that she was to go to bed for a good night sleep.

Feeling better after the shower and some more food Sam sat on the couch she had fallen asleep on. Ready to make a plan for her self she thought tomorrow she had to talk to Jack and make things better. How she didn't know but they were friends at least before all this mess she hoped they could go back to that.

Pete was another story she had to earn his trust that was if he ever talked to her again.

Thinking that she should call Pete, she picked up the phone and dialled his number, waiting for him to answer Janet walked in with a cup of coffee. Mouthing a thankyou to her. Janet mouthed back "Who?" While pointing at the phone. "Pete!" Nodding Janet walked back into the kitchen to give Sam the private that she needed for this phone call. Pete answered saying bluntly "I am not ready to talk to you yet. Just leave me alone from awhile. Sam I love you but you" getting angry again "I am not ready!"

"I am sorry Pete I do love you! Call me when you are ready"

"OK" Pete replied hanging up Sam thought that was a good start. Now just tomorrow was going to be the hardest.

Jack just stood there watching Sam walk away hearing her last comment he was in shock. He couldn't believe he was right she regretted them spending the night together. It was special! Well at the time he thought it was but now he just felt sick to his stomach he felt ashamed. Lowering his head he went to the lockers grabbing his keys, wallet and anything else he needed and headed to the elevators determined to go home. Getting to the surface heading straight for his truck it was like he was in auto mode not concentrating on what he was doing.

Pulling into his driveway not really knowing how he got home without having an accident along the way. Opening the door shutting it behind him and heading straight for the cabinet where he kept his best bottle of Jack Daniels. Hoping to block out the rest of the world and the problems, hurt and anger that now has built up inside him.

Jack had been sitting there for hours not knowing what time he got home but it had gone dark outside which made it black inside the house which matched his mood. Speaking out load "I should turn on the lights" then thinking nope I like it dark I can think better. Which he was starting to think about what he is going to do, he couldn't see her or work with her knowing what had happen and that she thought it was a mistake. But what options did he have? Then remembering his conversation with Hammond about a month before him and Sam "STOP thinking about it". Hammond had called him into his office one Monday morning.

_**Remembering**_

Jack I know how much you love this place but I have an offer to make you. Hammond started.

Getting Jack's attention he sat up straighter looking very intrigued at what Hammond was about to say.

You know that the Alpha Site is now finished and up and running the best we can.

Jack looking a bit puzzled. The General continued "Well the joint chefs have decided that we are going to start up another site named Stargate Beta Site! They want you to run it!

Shocked picking his jaw up off the floor he said the first thing that came to mind.

I won't be on SG1! More of a statement than a question but George answered anyway "No you wouldn't be" Continuing "You would live off-world at the Beta site only coming back to earth to report every 6 months" You would be in charge and reporting to me every week but to the President, Pentagon and Joint Chefs every six months. You don't have to take the position but please think about it? Dismissed!

Getting up to leave Jack turned and asked "If I take the job who will be the new CO of SG1? Hammond replied "Major Carter!" Smirking he thought of one more question "When would I be going?" Hammond smiling "3 Months Jack that's when we expect everything to be functioning to start moving personal out there permanently."

Leaving Hammond's office and walking to his office thinking should he take it or not realising he hadn't even asked what planet it was on. Laughing to himself did it really matter what planet.

Jack had turned the position down about 3 days later saying he didn't want to leave SG1 just yet. Hammond was disappointed but knew Jacks reasons were valid.

_**Present Day**_

Actually speaking the words "Sounds good" Feeling his mood lighten a bit he thought some more about it, no SG1 in turn that meant no Daniel no Teal'c "damn" he still wanted to see them but then that meant he would have to face Sam every day "I can't do that" So deciding that Daniel & Teal'c could come to the Beta Site when ever they are needed he could request that they visit for some new rock or tactical help "that could work". Deep in thought trying to imagine him in charge of the Beta Base he wasn't sure if he could do it, "For Crying out loud" your Jack O'Neill you can do anything. Happy with his decision he put his bottle of Jack Daniels away and heading towards his room for a shower and a good night sleep as he had to approach General Hammond hoping no one else had been offered the job. If they had he would just retire or transfer to the Beta site to head a team there. After the shower and more thinking he slipped into his bed and let sleep take over him having feeling like the world was just taken off his shoulders for the first time since the, as Sam said MISTAKE.

_**Jack Next morning**_

Arriving the next morning feeling a lot better about the decision Jack had made knowing it was the right thing to do and the sooner he approached Hammond the better. After going to the lockers to change into his BUD's Jack headed towards General Hammonds office determined to get this job or retire but not leaving his office till something was worked out.

Walking through the control and briefing rooms towards Hammonds office he notice the General was only signing paper work so it was now or never, knocking on the door seeing the General wave him in Jack took a deep breathe which didn't pass George. The General thought "What now I don't need more trouble I have already split the team. Don't tell me he's going to leave. Hoping it was anything but that. George had noticed the tension between the Major and Colonel and felt it was his fault but it was his job." Jack not taking a seat like he normally did choosing to stand.

"What can I do for you Colonel?"

"Am Sir how is the Beta Site coming along?" Jack thought that was a good start!

"It's about a month off completion! So on schedule, but we are still looking for a Base commander." Hammond started to get the picture.

"Sir? Is the job still open to me? Sir! Jack sounding hopeful.

"Take a seat son!" Jack doing so relieved some of the tension in the room.

"Sir I want the job! It is either that or I retire!" Jack stated up front.

Hammond a little shocked at the abruptness in the Colonel's statement.

"Is it that bad Jack that you want to leave?"

"Sir the only reason I didn't take the job was SG1! SG1 is no longer together so what is keeping me here? Nothing!" Waiting for Hammond's reply again feeling his hands sweat.

"So I guess this is my fault for splitting up the team!"

"No Sir just circumstances have made it hard and I have done enough damage as it is time for me to leave." Jack replied in a sad tone in his voice that he was hoping Hammond didn't pick up.

"Jack have you and Sam talked at all?"

"Yes Sir we spoke yesterday."

"Can you work it out?" You seemed to be dealing with it for the first 3 weeks?" Hoping there might be a way to sort this out. He wanted Jack in the position on the Beta Site but on good terms not like this.

"No Sir! I'm the reason Pete called off the wedding. They sent him the photos".

"Sorry Jack I didn't know."

"Sir I just want to forget it every happened and concentrate on something good. I think the Beta Site will be good for me. It's something I can put 110 into."

"I will make a few calls and get back to you when I have an answer."

"Could you do one more favour Sir? Make her CO of SG1?" Jacks words all most a plea. Hammond nodded replying "I will see what I can do!"

"If it all goes through can we not inform anyone until I'm ready Sir?"

"I can do that son! Dismissed"

Jack leaving the room headed for his office deciding that he would get his paper work all out of the way and head home early.

Sam had spent the next day trying to find the Colonel but luck was not on her side. She knew he was here because the sign in book he was one name above hers. Going to his office to see if he was there, that had been where he was hiding for the last week. But nope so she tried the Commissary, Control room, Gym room, Daniels office, Teal'c quarters, his quarters even her lab but no one had seen him. She needed a break so she went and sore Janet. After spending an hour with Janet she headed back to the Colonels office hoping he would be there but no he wasn't there. Thinking maybe he had left the base already she rang the front gate to see if he had signed out, according to them he had about five minutes ago so she missed him all day going all over the base looking for. I suppose if he wanted to hide he would know where no one would find him. Sighing she gave up went to her Lab to do the work that she was supposed to be doing, instead of looking for him all day.

The next day Sam had been waiting for him in the SG1 lockers. They had to talk now before it got any worse. Sam tried to approach him. "Major I think we all have a briefing to go to. As I am late I have 5 minutes to get ready so leave now so I can get dressed." Using ranks got her attention and the way he said it. Obviously he wasn't ready to talk either. Sam snapped back a "Yes Sir!" turning on her heals and walking out hearing a slam as she closed the door behind her. This is not good from what she can tell this was going to be a 10 to 14 day mission. Only good thing is that her dad was there. This briefing was just to clarify what teams would be going knowing the General he will send SG1 for sure. SG9 would be going because of her as Freya wanted Sam to see some new technology that they have. "Oh this is going to be fun!" Colonel not talking to her, Dad's going to know I am not on SG1 and be asking questions and if that wasn't enough I have to put up with Freya. The briefing was short Sam was right SG1, 2 and 9 will all be going to help the Tokra move to another planet.

The next two days Sam was busy with her new team mates this was there first mission together and she was nervous. No one had asked why she was transferred but they all knew as the rest of the base. Gossip was quick in this place and it could be stoped. She liked her new team mates but they were no SG1. SG1 plus Janet were family until recently no one could break that but themselves and that had what happened. Sam and Jack broke the rules now Daniel and Teal'c were paying for it too.

Daniel, Reynolds and Colonel Conner (new leader of SG9) arranged for everyone to have breakfast together the day before the mission so we could get to know everyone. SG1 and 2 knew each other well but SG9 was newly formed as they had taken some casualties and there Captain was on Maternity leave.


	2. Grounded

_**SECOND CHAPTER**_

The morning of the third day since Jack's request, Jack, Daniel, Teal'c, SG2 and SG9 which included one Samantha Carter all sat around 2 tables in the commissary discussing there next mission. They all were to go and help the Tokra for 2 weeks moving to another new planet as they had feared that there current one was exposed.

Jack not paying any attention to the conversation at all just playing with his oat meal failed to notice an airman standing beside him trying to get his attention. Daniel giving Jack a little jib with his elbow getting Jack's attention while he pointed to the young airman.

"Sorry Airman what can I do for you?"

"General Hammond would like to see you in his office straight away Sir!"

"Thank you" Jack replied getting up from his chair.

"Jack?" Daniel looking at him questionably.

"It's fine Daniel I know what it's about"

"And?"

"Bye Daniel, Guys" with that Jack turned on his heals and left, leaving questions on everyone minds.

"General you wanted to see me Sir"

"Take a seat Jack!"

Making sure no one heard this conversation sending the airmen further down the hall and closing the door behind him Jack took a seat opposite the General.

"I have received an answer from the Joint Chefs and The President. Your request has been accepted, they also agree with your recommendations to put Major Carter in command of SG1; despite the recent events they think she is the perfect person for it. Congratulations Jack you now are the Commander of the Beta Site!"

"Thank you Sir. I know you had a lot to do with this." Hammond giving a small smile.

"Well there are going to be a few changes to the next mission that SG1 is going out on tomorrow." "I will put Major Carter in charge of SG1!"

"Sir are you going to tell them that I am leaving?"

"No! I think that is your job Jack! Waiting for a response Hammond realised speaking to Jack in a low tone that spoke volumes "You're not going to tell them are you?"

"No Sir I think it is better this way!"

"I hope you are right son!" Hammond shaking his head continued

"Ok this is what we are doing you have 1 week as of today to do all the final paper for SG1 and organise everything you will need for your new position, then you have a week downtime to organise any personal matters. Is that enough time for you? You will be going to the Beta Site as soon as your back to start receiving your personal through the following day!"

"That is perfect Sir I will be here in 2 weeks ready and looking forward to it Sir!" Jack said in a cheerful tone.

Hammond smiled gave Jack a nod and said "Dismissed!"

As Jack was leaving he thanked the General one more time.

"SG1, 2 and 9 please take a seat!" Hammond said getting this briefing under way.

"Is Colonel O'Neill joining us Sir" everyone wanting to know where he was as no one had seen him since this morning when he was summoned off to the Generals office.

"No Doctor Jackson, Colonel O'Neill will not be going on this mission!"

"Sir?" Daniel questioned

"The Colonel has too much paperwork to be aloud off-world at this point, he has been given one week to complete all his paperwork and then he is taking one week personal leave. Now that you know what he is doing do you think we can start this meeting Doctor Jackson?" Hoping that would put a stop to all the questions.

Seeing that everyone at the table were all trying to hide a smile Hammond thought that worked well they all think I have grounded him for not doing his work. If only they new that he always had the report typed up on time but just handed it in late so that no one found out how smart this man really was and to annoy me.

Forcing his attention back to the briefing Hammond realised that none of the people before him will be here when Jack goes through, as this was a two week mission and they leave tomorrow that would bring them home a day after Jack has gone. After a long briefing Hammond Dismissed everyone heading to his office to take a break that was needed after what seemed to be along day.

"Well that was interesting. Congratulation Sam, you get to order Teal'c & I around for the next 2 weeks." Daniel teased.

Sam just gave a small giggle and kept walking "Whose hungry I am going to the Commissary?" Looking around seeing all the nods and Yes Sir's as they all smiled everyone had noticed since Jack wasn't around for the meeting and wont be coming on the 2 week long mission, Sam's mood had gone from solitude and quiet to happy and joining in the conversation. Teal'c feeling that there is more to O'Neill not coming along to the Tokra home world decided to go and see him. "I will not Major Carter I'm going to see Colonel O'Neill." With that Teal'c turned and walked down the corridor towards O'Neill's office. Everyone else was heading for the Commissary knowing that this afternoon they all had to get geared up as they were heading out at 0600 hours.

Teal'c knocked and opened the office door not waiting for a reply. Entering he noticed Jack's desk was full off files. "O'Neill I do not believe you are grounded for not doing your required paperwork and that this is extra paperwork." Smiling, Jack looked at his friend knowing that he could not fool him.

"Take a seat!" Doing so Teal'c new there was more.

"Teal'c what I'm about to tell you does not to leave this office! Understand?"

Replying "Indeed"

"I am leaving! Not the SGC just Earth, I'm the new CO of the Beta Site."

"I will be reporting to Hammond every week by transfer but only coming back to earth every six months to report to the President."

"Why have you not informed us of your decision O'Neill?"

"Cause it's easier to go this way!"

"Are Major Carter and Daniel Jackson not your friends and deserve the right to be told you are leaving?"

"Yes Daniel is my friend and he will understand." Getting frustrated with the conversation "Major Carter and I are no longer friends Teal'c and never will be again!

"I believe this to be untrue O'Neill"

"Sorry Teal'c but I have a lot of work to do." With that Jack gave a wave as a dismissed gesture.

Getting up from the seat Teal'c looked at O'Neill.

"It was an honour O'Neill, you will be missed!" leaving Jacks office heading for the commissary to join the rest of his team.

Arriving at the Commissary Teal'c grabbed a plate of fruit and took a seat next to Daniel.

"How is he?" "O'Neill is well Daniel Jackson!" "That's not what I meant Teal'c!"

Teal'c only reply was "Indeed" Everyone looked at him knowing this is Teal'c way of saying something is up and that he knows what it is.

"Well are you going to tell us?" Daniel looked at him curiously

"It is not my place to say!" was the answer returned.

Daniel gave up knowing Teal'c, he would get nothing.

Vowing that he would go and see Jack before he left in the morning for their mission.

Daniel looked at Sam with a questioning eyes and only getting a shrug as she looked at her now empty plate.

As it turned out Jack wasn't on base that afternoon he had been called over to the training camp for SGC personnel and Daniel had missed him. Daniel rang Jack on his mobile but Jack had said he was busy and would talk to him when Daniel gets back from the mission. Accepting this for now Daniel had no clue that Jack wouldn't be here when they got back.

Beta Site was one of the biggest secrets around at the moment no knew about it. The only people that knew were the ones that were going to go there. It was kept quiet due to the politics that surround another site running off world. Jack and his new staff were due to leave in 14 days. Not even the team leaders that were going to lose one of there members new.

Sam had been worried since Teal'c and Daniel's conversation. What is he up to, he never missed a mission and General Hammond has never grounded anyone other than medical reasons. What if Jack is sick? No he would see Janet and she would tell Daniel or me. Not going to find out any time before the mission she promised that when she gets back she would corner him till they talk every thing out and were friends again. She was still glad that he wasn't going on the mission with them because she didn't want this tension to interfere with the job, and there talk would have to be out of the mountain and somewhere they could talk openly. If she could get him to talk at all! She mused. Sighing she headed towards her quarters to get some sleep before they left at 0600, she hated early starts.

As the Walter announced over the PA "Chevron Seven locked" and a big "Kawoosh" as the gate came to life. Hammond said "SG1, 2 and 9 you have a go and god speed" Sam turned "Thank you Sir" Looking up at the control room noticing Jack standing there watching them leave. They locked eyes for a moment and as Sam gave him a small smile trying to tell him that they would be ok he turned and walked away with the military face that he had perfected over the years, hiding all emotion.

Jack headed up to the briefing room to watch as she stepped through he didn't mean to get caught watching her but he could do nothing about it now. This was his last chance to look at her. He loved her with all of his heart and with resent events his heart now broken into a thousand pieces.

The next week went fast he had completed all the final arrangements for the Beta Site now all he had to do was the personal stuff. Heading out for his week leave he ran into Janet at the elevators. "Heading off Doc" Smiling Janet looked at Jack and sore that he too was warn out. "Are you ok Sir?" "Yeah I was wondering if Cassie is free to spend a couple of days with me, maybe later in the week. I know she is in school but I could do with some company. I'm going to my cabin day after tomorrow for 3 days I would love for her to come?" "I will ask her Colonel I'm sure anything to get out of school." They both started to laugh as the elevator came to a halt. Both walking to there respected cars Janet called out "I will get her to call you tonight, if that's ok?" "Yeah I will be home!" With that Jack opened his truck and started to head home, he had started to pack his things already so there wasn't much more to do other than put it on the market, once everything was put in storage. He had selected what he wanted to take with him and most of it was in his base quarters. Jack had spoken to Sara and asked if she wanted anything but she declined saying that she had everything, they had talked for hours that night and Jack had told her about Sam, he asked her to look after the sale of his house and what he wanted to do with the money. He already lined up someone to buy his truck and motorbike so all that left was the Cabin which is why he was going up there. Janet had rung that night saying Cassie would love to go and organised anything that she would need while she there.

Jack had picked Cassie up at 0400 and where now driving along the highway. Cassie had slept till well pass 0900 and was not putting her favourite CD in the player. Lucky for Jack it had been a band called Matchbox 20 which were pretty good. Cassie told him all about the latest gossip at school and her new wonderful boyfriend.

By 4 in the afternoon they had talk, well truth be told Cassie had talked all the way about everything going on in her life, now it was Jacks turn. "Cassie? Lets get all the stuff inside then I will take you for a tour and cook up a couple of steaks! Sound good?" "Yeah sounds great" Cassie so excited running off like she used to when she first came to earth.

"Now that is done lets go for a walk around the lake!"

"Sure" as they started to walk Jack started to tell Cassie all the interesting stuff.

"Cass I'm not good at this but I'm going to try ok? I am I think of you as my daughter the one I never had! And this is harder than I thought!"

"What's going on?"

"I'm leaving earth! I got a promotion; I'm going to be in charge of another site, on another planet!"

Cassie stopping with her jaw wide open tears starting to form "You can't go!"

"I have to Cass it's for the best, I want you to have this place. If you don't want it you can sell it I can give you some names of some people who will help you find a buyer."

"Jack I don't want you to go why is it because Sam's marrying Pete"

"No Cassie it's not but it is because of my feelings for Sam, we can't do it anymore both of us!"

"Do they know you are going does mum know?"

"No and I'm not going to see them before I leave now!"

"When are you going?"

"As soon as we go back!"

"I want to keep it. I like what I see so far! But I don't think I will be fishing maybe swimming but no fishing!" both bursting into laughter Jack grabbed Cassie and gave her a big hug.

"I love you as my own daughter and I am very proud of you!"

Bursting into tears again Cassie said "I love you too and I'm going to miss you."

Moving from their position they walked around the rest of the lake and cocked up those steaks Jack had been talking about.

Over the next couple of days they talked played around have water fights swimming Jack even got some fishing in. But most of all Jack told Cassie all about the cabin and its importance to his family.

Arriving back home both sitting in his truck out the front of Janet's place, knowing that this is the last time they will see each other for a very long time. They hugged saying their goodbyes. Jack had asked that Cassie kept it to her self till after tomorrow. She agreed not liking it but agreed.

As Jack had already put his house on the market so his last night on earth he was staying on the base.

By 0600 the next morning it had gone around the base that Colonel O'Neill was leaving, the Beta Site was not a secret anymore. Everyone was giving him their best, good luck's and it was an honour Sir as he was walking into the infirmary to get his last physical all the nurses cleared the room. Obversely Doc knows he sighed knowing this was going to be painful, when Doc was angry with you she bought out the big needles.

"I can't believe you are leaving without saying goodbye." Was Janet's first comment

"Doc you know why I can't! And don't blame Cassie I made her promises?"

"Cassie knows?" Janet looked in a state of shock!

"I guess Cassie didn't tell you then?"

"No! It was one of the nurses!" she replied. Realising Cassie new

"That's why you took Cassie up to the cabin to say goodbye?"

"Yeah and give it to her!"

"What?"

"I gave Cassie the land and Cabin! I have organised a guy to up kept the place and it is all paid for!"

"I have also told Sara to give the rest of the money from the sale of the house to Cassie for you to put into a trust fund for her!"

"Jack you can't!" Janet yelled in total shock  
"Yes I can she is like a daughter to me and I have no one else to give it to!"

Janet and Jack discussed a lot of things over the next half an hour as she was doing the physical.

When Janet had finished she looked Jack in the eyes with a sad expression.

"We are going to miss you Jack!"

"Are you ever going to come back?"

"I have to report to the President every 6 months, so six months it is!" smiling at Janet

"Surprisingly I'm going' to miss ya Doc!" pulling her in for a hug embracing as friends.

Letting her go he headed to the lockers to get ready.

Walking into the gate room in full dress blues, it looked like every person on this base was in the gate and control rooms. Janet noticed that Jack had a star on his uniform. He had been promoted to Brigadier General. As Jack walked to the base of the ramp where Janet and the rest had lined up. He had to walk past everyone to get to this point as he past each SGC member they saluted him with respect that Jack thought he didn't deserve. There was not much room in the gate room from the personnel that were going through with him and the ones that were saying goodbye.

Walter announcing over the PA each Chevron as it locked, as the gate came to life Jack turned around to watch it, it was his favourite part, other than stepping through it. General Hammond walked up to Jack and held out his hand. "Good luck son and God speed" "Thank you and I will have my report done in seven day Sir" Jack said smirking as he saluted the General returning the gestor Hammond saluted thinking that man will never change!

General O'Neill turned to his personnel addressing them "Beta Site Personnel move out turning around Jack put his sun glasses on "see ya later Doc" Janet shaking her head "Yeah see ya Jack!" Looking over his shoulder at Janet he smirked as he walked through the event horizon. With that Jack O'Neill was gone. Leaving his best friends and the woman he loved behind and they didn't even know!

Guess they will find out soon enough! Janet mused heading back to the infirmary. She was going to kill Cassie for not telling her.

_**END OF SECOND CHAPTER**_


	3. So not good then

**Sorry this is only a short chapter. I am hoping to get more written tomorrow.**

………………………………………………………………………………………………………………

As Sam walked out of the Event Horizon she felt a little queasy in the stomach something she hadn't felt in a long time, trying to shack it off she sore that her dad and another Tokra were there waiting to great them. She smiled, happy to be seeing her dad. Walking up to Jacob, Sam put her arms around him and embraced him.

"Hi Dad good to see you again, and we get two weeks together!" she happily said

"It's great to see you to! So how you going?"

"Have been better dad!" Seeing that questioning look she was receiving from Jacob.

"Tell you later!" shaking her head no, not wanting to inform him of the past couple of month's events.

So accepting that for now, obviously she didn't want to tell him in front of everybody.

He asked "So where's Jack"

He heard Daniel give a small laugh behind Sam.

Looking over Sam's shoulder at Daniel, who in turn tried to explain that Jack had been grounded because he was behind in his paperwork!

Jacob giving a smile shaking his head, thought that man was impossible and asked himself and Selmac how George ever handled him?

They headed to the transport rings and transported into the underground base, SG1 had a briefing with the council within the hour and they had to been shown to their quarters for the next few nights. The briefing had been a long and everything was planed for the move.

Sam was to help the equipment for the science labs to be moved then she was to stay at the new home world to study some of the newly required technology that Freya has found.

Teal'c would be back and forward to the gate helping with the heavy lifting and making sure everything was in order before it went through. Daniel was to go to the new home world the next morning and translate some of the writing in one of the ruins on the surface. As it was in Ancient Daniel was the most qualified.

Jacob had made sure that Sam's and SG1 quarters were near his so he could visit with them and catch up on the gossip at the SGC, he had no clue what he was about to be told. After the meeting Sam said that they needed to talk and she wanted to do it in his quarters, as it was personal.

"So Sam what's going on and what is the real reason Jack's not here?"

Jacob started wanting to get straight to the truth.

Giving a small smile Sam instructed Jacob to sit and listen to everything before he exploded.

"I have been taken off SG1 I'm now on SG9!"

"What!" Jacob yelled

"Dad please listen its complicated!" she said in a tone that told him this was going to be a long night.

"About 2 months ago SG1 went to this Planet, it was primitive compared to earth but they had plants that could be used for antiseptic. The villages were friendly so we stayed with them for 3 nights." Sam took a deep breath

"On the last night we had a party to celebrate the treaty. We ate and drank all night; the drink we were drinking was like fruit punch with Vodka in it but more toxic so we found out. It was special liquid that acts like a virus. We had a hangover from a hard night drinking other than that we were good. We didn't know what the virus would do. We know now that it takes about 48 for it to go through your system then you are ok again." Avoiding what the virus did Sam just look at her dad this was hard she didn't want to disappoint him but what was done was done and she had to tell him before someone else did?

"Sam what happened?" Jacob new this was hard for her he could see it in her eyes.

Taking a deep breath again she answered

"The virus affects the brain; it takes away all your inabissions, just like alcohol but a lot stronger."

Giving a small giggle she continued "Daniel didn't do anything to bad he trashed his office told a few people what he thought, kissed Janet that sort of thing basically just played around. Teal'c wasn't affected we guess because of him being a Jaffa!" Sam paused long enough for Jacob to say

"So what did you and Jack do?"

"Am… we….. Um….. We slept together!" Sam said looking away in shame.

"You slept together" he repeated

"Yes"

"So how did you get caught? I'm guessing that is why you are no longer on SG1?" he asked in a tone that spoke volumes he wasn't happy at all. Sam guessed that Selmac was keeping him calm.

"Some one was stalking out my house they took photos and sent them to General Hammond and Pete?"

"Pete how did he react?"

"The wedding is off, he is angry but said just give him time before we can talk again. I am going to ring him again when I get home. I love him and want to make it up to him." Sam said in a hopeful tone.

"What about you and Jack? Is that why he is not here?" Jacob just not believing what he is hearing.

His only daughter sleeping with her CO.

"We have spoken once since I was taken off SG1, it didn't go well. I'm going to try and talk to him when I get back as well; we were friends doing ok with the situation, now he can't stand to be in the same room as me. I said some hurtful things. I was upset and didn't mean them the way that they came out. But I do regret sleeping with him! It should not have happened!" Getting upset again Sam could feel the tears welling up in her eyes.

"He will understand!"

Knowing Jack he would take it to heart and be very angry but he could see Sam was upset already and no point in telling her that they would most likely not be friends again. She was being hopeful that they could work it out. Jacob new about the feelings that Sam and her CO had for each other but had always played by the rules. Now Sam was trying to fool herself that she didn't have feeling for Jack.

Jacob didn't like the fact that Sam and Jack had spent the night together. And that she had been taken off SG1 but this wasn't good! Sam in denial about her feeling is just going to make things worse for her and Jack. He felt sorry for Jack he knew that Jack was in love with his daughter and being told that she regretted the night they spent together would just break his heart. Talking to Selmac he said Jack would never show it though, Selmac agreed!"

"Dad! I'm tired, I'm going to go to bed we have a big couple of days. We will talk more later, ok?" Sam said as she got up and left.

Jacob needed to know more so he headed for Daniels quarters to have a chat with him.

As Jacob walked into Daniels quarters Daniel held out his hand as top stop Jacob from saying a word.

Daniel started "I don't know Jake! Jack won't talk to anyone about it. They were working through it until Sam was taken off SG1. Jack had a huge fight with Hammond and got thrown into the brig over night. Sam doesn't know that by the way! He hasn't talked to anyone much unless it is business. Then you are pushing it. In the last week Jack hasn't been on base much just coming in to his office doing paperwork then going home early and the General hasn't said a thing. Normally Jack is on base more than Sam and I but no one has seen him. Teal'c spoke to him yesterday but won't tell us what he knows." Taking a breath Daniel finally let Jacob get a word in.

"So not good then?"

"No! Not good at all!"

"I think I will return to Earth with you. I need a vacation and this needs to be sorted before they both do something stupid!" with that said, Jacob turned and left Daniel smiling. If anyone could get Sam and Jack to talk it would be one General Carter.


	4. Realisation

**A/N** _Sorry this is not a very exciting chapter but the next 1 starts to get better. Hope to have it up very soon._

_Reviews help as this is my first fic._

_**FORTH CHAPTER**_

Over the next couple of days everyone was busy with the move, Sam had gone to the new home world with Freya and her dad. The move was almost completed; all that had to be done was collapse the Tokra tunnels on the old home world. Everyone was more relax and were finding more time for what they were assigned to do.

Sam had been working in the lad all day and started to feel queasy in the stomach again. She had been getting queasy everyday but only been sick a couple of times. She had been sick early morning or late at night so no one had noticed. She had thought that maybe she had caught a virus or a stomach bug, but as the feeling didn't go away and she was getting it bad every time she was around food, Sam started to get nervous. Sitting on a one of the stools happy that Freya, dad and the other scientists had taken a break to get something to eat. Speaking out loud "I can't be? Not now! Not possible!"

Trying to calculate the timing but not liking what answers she kept coming up with. Pete had been out of town for the three months before and only seeing him twice at the beginning of that time. Then when he had come back for a week, that's when he found the photos and all hell broke loose. That left one option and that wasn't going to go done well. If she was pregnant it would have to be Jack's. Sam wasn't an expert but everything she knew about pregnancy was that morning sickness happened in the first trimester. She had been with Pete then about two months later she slept with Jack. That meant if it was Pete's she would have to be least four months. She would have to ask Janet to do a test as soon as she got home before she spoke to either of them. "Why me? Why did this happen now?" The more she thought about it, it made sense that she was pregnant all the queasiness and being more tired than normal.

Jacob noticed that Sam had not moved since they left for lunch and was in deep thought.

"What are you thinking about Sam?"

"Nothing dad! I'm just taking a break tiring to relax and enjoy the first peace and quiet I have had since we got here." She replied with a smile.

"So have you had any luck with the thing sitting on your bench there?" Jacob questioned.

"No we have hit a wall with this one. We can't get it to turn on and there is no energy coming from it. There is so much else to look at we decided to leave it."

"Ok any thing I can do?"

"Yeah leave me alone so I can get back to work?" smiling she continued

"Come and get me for dinner. We can have dinner and maybe take a walk on the surface?"

Nodding in agreement Jacob waved a goodbye and went on his way to have another chat with Teal'c.

Teal'c was in Kelnem when Jacob interrupted him.

"So Teal'c are you going to tell me what you know?"

"I will not divulge that information. I have promised O'Neill that I will not."

"Teal'c they are not talking and I am afraid of what Jack is doing is going to make the situation worse."

"It will not Jacob, O'Neill is doing what he thinks is best for him and Major Carter. I will not discuss this any more!" " Everyone will know in a couple of days." With that Teal'c left leaving Jacob astounded at Teal'c loyalty to Jack.

Teal'c was getting annoyed at everyone didn't they understand, he was not going to tell them. He couldn't, it would betray O'Neill's trust.

That night Sam and Jacob took that walk. Sam was quite she wanted to tell her dad that she thought she was pregnant, but her fear of what he would think and that maybe she was wrong changed her mind. They kept the conversation at general talk. Talking about Mark and planning a little time together when they leave in two days. Jacob had organised two weeks on earth before he left for a three month mission. Sam was happy with that, she could talk to Jack and then have two weeks off and decide what she is going to do if she is pregnant. She was going to need her dad there to get through this especially if she was right. They enjoyed the walk and headed to bed for there last day with the Tokra.

The next day was busy inspecting the last of the technology and packing all the gear to go back to earth.

That night there was a feast put on to thank the SGC staff for there help in the move. There was no more mention of Jack that day and Sam was happy have all the questions stop. Sam had relaxed a little and enjoyed the night with her friends and family.

On the last morning with the Tokra, it had started the same as the last five days in a row, with Sam's head it a bucket loosing her small breakfast that she had managed to eat. They quickly did the final packing and headed for the Stargate.

After Daniel dial home everyone had step through the event horizon, Sam took a final breath as she walked through. Thinking about Jack and the conversation they had to have, also hoping that she didn't loose her stomach contents on the other side. Sam appeared out of the blue shimmer and took a deep breath, looking for the Colonel as General Hammond ordered Jacob and SG1 to the briefing room immediately!


	5. Things not said

**A/N – **Hope you are liking this so far I'm trying to get the chapters up as quick as I can. Reviews are good when the review stop I will stop writing this story so keep the reviews. Sorry about Gramma or any spelling mistakes.

If you have any suggestions on how you want the story to go let me know.

**CHAPTER FIVE**

"SG1, 2 and 9 welcome back! Good to see you Jacob!" General Hammond started towards Jake to shake his old friend's hand. He continued looking at SG1 "Jacob, SG1 briefing room now please? SG2 and 9 your briefing will be at 0730, dismissed!" Walking at of the Gate room with Daniel, Teal'c directly behind him, Sam and Jacob catching up after Sam had handed over her pack and weapons to one of the SF's. Walking up through the control room into to the briefing room there were files on the table marked BSC. Daniel saw the files and immediately asked "What's going on General?" Dr Jackson, everyone please take a sea?"

George started by saying "Jacob this is top secret and I would appreciate if this went no further than this base? The Tokra council are not to know about this as there are still issues with the Trust. The folders in front of you are classified. They have only now been allowed to be made public to the SGC staff."

He had full attention of the room. "Six months ago a small committee was formed and decided that the Alpha Site was good for Earth as a back up but it was felt by all that it wasn't enough, so plans were drawn up and passed to build an identical base to the SGC "Beta Site Command". It was completed last week and the personal started to go through yesterday."

Daniel knew what had taken place. "Sir where's Jack"

"General O'Neill has taken command of the Beta Site. He was the first permanent staff to go through."

"He was offered this job four months ago but turned it down. We were still having trouble filling the position when Jack asked for the position three weeks ago."

"He knew he was leaving and didn't say anything!" Daniel yelled in frustration.

"Teal'c you knew he was going he told you! Daniel accused him

"Indeed!" was all Teal'c replied

"Daniel Jackson please calm down or I will have you remove from this briefing" The General stated in a strong and annoyed tone.

"Sorry Sir!" As Daniel retook his seat.

Everyone else had remained quiet and were all in there own thoughts.

"The BSC will have 5 teams BS1 to BS5. BS1 is their front line team as SG1 is here. BS2 and BS5 have Scientist and will be mainly survey teams. BS3 Marines and BS4 are the research teams. They have there own CMO and have an Iris over their Gate as well. "I want all of you to read up on the Site and brief any changes you recommend. This is to stay quiet as possible for now. The Trust already have tried to infiltrate the site." "General O'Neill will be sending a weekly report through to myself and every six months he will return to Earth to report to the President and the Joint Chefs."

"Ahhh! General when and how did Jack become a General with everything that has gone on I thought that advancements were now going to be very hard for Jack and Sam?" Sort of confused Daniel asked

"Well that is the good news I had to inform you all of. Congratulation you are now the leader of SG1 and as of last Thursday you are also promoted to Lt Colonel" Hammond announced with a big smile on his face.

"Congratulation Sam!" Daniel said as he looked at her and smile to say he was pleased.

Sam's mouth just dropped she couldn't believe this after being taken off SG1 now she was the CO of SG1 and being already promoted to a Colonel.

After every one had said there congratulations and about times they all took their seats.

Daniel still couldn't believe Jack just left without saying goodbye.

"Sir I was just wondering if you knew why Jack just left and didn't say goodbye or tell us himself?" He didn't want to hurt Sam but he needed to know, he thought that Jack and him were good friends and that he would confide in him.

"I don't know son, only he can answer that! He hasn't spoken to many people at all. I know he took Cassie to the Cabin. Maybe she might know more!" Hammond could understand why Jack left but it was still wrong to leave without saying goodbye.

"One final thing, we have a Kerri Johnson flying in from the Pentagon tomorrow to brief us on her investigation. She then will be escorted to the Beta Site to interview all staff."

"Sir who will be escorting Ms Johnson" Sam asked hopeful that SG1 would be signed the mission but no such luck. "The rest of the BSC personnel, Lt Colonel Fretti and his new team." Hammond stated as he got up from his chair. General was just about to dismiss everyone when Walter walked in and announced that General Hammond had a phone call that he had to take. "You all have two weeks down time, I will see you all back here for your first mission then. Oh and Colonel I am ordering you not to set foot in this mountain unless I request you here is that under stood!

"Yes Sir" Was all Sam could get out.

"I believe that you are required in the infirmary for your post mission check up. Dismissed"

Everyone stood up and started to leave. "Daniel! You, Dad and Teal'c all go get checked out I'm going for a long needed shower!" "Are you ok Sam you are looking a little pale?"

"No I'm fine just a bit worn out and then getting this news I just need a shower and then those two weeks off." With that Sam left and headed towards the lockers.

Jacob had kept really quiet and Daniel was wondering if Selmac had taken over to keep Jacob from saying anything inappropriate. Jacob, Teal'c and Daniel all headed to the infirmary for their check up so they could be released to shower and leave the base as well.

There had been a few people along the corridors as Sam walked to the locker rooms. When she entered she was glad that no one was in there. Everyone just looked at her as she passed, all looking very sad as if someone had died. When she got to her locker she opened it and just stared into it. She was trying to keep all her emotions in check. Feeling like something was just going to take her over the locker door she was holding on to slammed shut with such force that it opened again. Getting even more frustrated she started to grad her shampoo and conditioner. Not forgetting her towel Sam walked into the showers and put all her gear down on the shelf, turning on the hot water Sam just couldn't believe that he was gone.

Her blood had been boiling in the briefing room, she was lucky that she didn't throw up across the table, she had to fight her body to do as it was told.

As Sam turned on the cold her anger had hit boiling point, she got under the water and let the warm water run down her body, hoping that it would cool her anger. He just left no word to her or Daniel

He had no right to just leave her all alone, not now. Why did he leave she couldn't understand he wasn't the type to run away. As she picked up her shampoo lost in thought Sam pelted her shampoo bottle across the locker room. "You basted!" she yelled as she slide down the wall and curled her legs up to her chest sitting there in tears. She couldn't stop the tears running down her face.

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A/N - Next Chapter – Daniel finds out some of what Jack said to Janet.

Jack meets Kerri Johnson. There is trouble at the Beta Site.


	6. We broke the regs

_**CHAPTER SIX**_

As Sam sat there with her knees pulled to her chest and the tears running down her cheeks, being washed away by the hot water, not believing he was gone. Her mind went back to the night that has caused all the trouble.

It had been a normal day. All Sam wanted to do was go home and have a warm bath and a glass of wine and enjoy a quiet night. Pete was still away, and she had her house to her self. But that had changed as soon as she pulled into her driveway.

Pulling into her drive Sam noticed the big Black F350 parked out the front with the owner of the vehicle leaning against the bulbar. She couldn't help it, but stare at his form. Dress in his casual clothes, he was a very handsome man. She had seen more of him in the lockers but in his civvies her mind worked overdrive.

Sam locked up her Volvo and walked to the front door. Walking across her front yard she greeted the Colonel with a smile and indicated that she was going inside and that he should follow her.

As she started to open her front door she turned and smiled at the sexy man standing in front of her. "Hi Sir! What can I do for you?" was all she could say before she had Jack's lips on hers. His hands cupping her face and he gently rubbed his thumbs along her cheeks, all while not stopping the kiss.

They stumbled through her front door, still kissing only stopping when they needed air. As they made there way down the hall into her lounge Jack nearly tripped a couple of time which made Sam giggle. "No giggling Major" in a playful tone. This only made her giggle more. Jack started undoing buttons on her blouse, she wonder what started this? Why was he here, doing things that she only imagined, why was she letting him?

His touch brought her out of her thoughts, sending tingles through her whole body, she started to lift his shirt up she couldn't stop but more importantly she didn't want to stop. Clothes were taken off and thrown around the room; they touched, kissed, watched and were lost in each other as they made there way to the bedroom.

As they got closer to the bed, the passion and intimacy got a lot more intense.

He laid her down on the bed and explored every inch of her body only stopping when he got a really good reaction. She rolled him over and explored every part of his body as well, neither one of them in a hurry so taking their time; they made love that lasted all night.

Sam opening her eyes felt a warm arm around her waist, she felt safe which is funny because of the out come, but she felt comfortable. She hadn't felt like this ever, she rolled onto her back leaving the arm around her looking at its owner she sighed. "It wasn't a dream?" She spoke out loud not meaning to but did anyway. "No it wasn't!" he answered as he opened his eyes. Looking at her he didn't know what her reaction will be and he felt her tense up under his arm.

"Why did you come over? Why did you kiss me? Why are you here in my bed? Oh my god! We broke the regs. What are we going to do? Pete?" Sam ranted as she jumped out of the bed taking the sheets with her leaving poor Jack butt naked lying on the bed. "Hey!" Jack started as they both realised Jacks predicament.

"Sorry!" Sam replied as she chucked her dressing gown to him.

Sitting up to cover himself Jack couldn't believe her reaction, well he could he just wished it wasn't.

"I…am …….sorry….I don't know what happened. I……….am think we need to get dressed!" Jack stuttered as he could feel himself getting aroused again just looking at her and the memories of last night. Sam agreed and left the room so Jack could get dressed. She still had the sheet around her when she got to the living room, realising that Jack's clothes were scatted all around the room she giggled to her self, they had fun last night! Picking up his clothes Sam heard the front door open "Don't be Pete, Don't be Pete!" thank god it was Janet.

"Sam it's just me!" Janet called not loud enough for Jack to hear, because as Sam greeted Janet (Jacks clothes in her hands) Jack came down announcing that

"My clothes must be down here cause there's not much of my cloths in your room!"

Sam lowered her head and Janet's jaw just hit the floor, Jack stoped dead in his tracks. Looking at Sam then Janet then at Sam again Jack saw his clothes in Sam's hands and pointed at them "Mine? I think I will go into the room to get dressed!" "You can have a shower if you like; the towels are in the hall closet." Sam replied.

"Thanks I think I will!" As Jack turned and walked away. He couldn't believe this caught by Janet.

"Um Sam you might want to go and get changed your self!" Pointing to the sheet that Sam was wearing.

"Thanks, I will, be back soon!" Sam said nervously.

Sam walked into her bedroom in a slight panic.

"What are we going to do?" Sam asked the room.

She got dressed and sat on her bed trying to get her thoughts together. No such luck though. She heard the bathroom door open and new that Jack was finished so she got up and walked out to the living room right behind Jack.

"Am Janet what are you going to do?" Jack asked not realising Sam was right behind.

"Sir how about what are we going to do we……we…..you know?" Sam still in shock.

"Ok both of you sit. I have made coffee and some toast. Both of you will eat and settle down." Janet started

"The reason I am here is because you both and Daniel have a virus. We didn't pick it up. We didn't know until Daniel started his little escapade." Jack and Sam both looked at Janet as if they were willing her to tell more. Maybe it was worst then what they got up to.

"So Doc what we did was caused by a virus. Like that Broca Divide thing?" Jack asked a little confused.

"Yes that's the best way to put it. You both are infected but it wasn't totally the virus it had to be what you wanted to! It works like alcohol but a lot more potent dose." Janet tried to explain.

"Am Janet are you going to report this?" Jack asked hoping that she wouldn't.

"Colonel I have to report that you are infected." Janet said in a sad tone but then it came to her "But I don't have to report the" she said waving her hands around hoping that they got what she was tiring to say "Doctor / Patient privilege. But you two have to talk this out before you go into work. I will give you half an hour before we have to go in!" She announced

"Why do we have to go to the Base?" Jack asked

"You still have the virus; I need to monitor your progress."

"But Janet can't we come in later give us a bit more time?" Sam pleaded

"Sorry Sam but NO!" Janet got up and left the house.

They had talk a little Jack said that he was sorry he should never of come around and that it was his entire fault. And he hoped that they could be friends still. Sam agreed that they will remain as friends but no one was to know because of Pete and there positions at work. That's where they left it, there was nothing said of regret just that they will remain friends and there relationship has not changed.

"WHAT DID WE KNOW!" Sam said as she came aware that she was still in the locker room showers. The tears had long gone and she felt drained.


	7. Need to Know

_**CHAPTER SEVEN**_

Daniel, Jacob and Teal'c all walked into the Infirmary, not really saying too much. Daniel was angry at Teal'c for not telling him but also understanding that if he had, it would be betraying Jack's trust and that was something Teal'c didn't do.

Janet was standing there waiting for them to come in; she just looked at them, sad but having had that talk with Jack knowing a little more about his reasons.

"I suppose you have been told?" Janet started

"Yeah!" was the reply from the three of them.

Noticing Sam not with them

"How did Sam take it?"

"Ok I guess she's gone for a shower she will be in after that!" Daniel replied

"I'll talk to her when she is ready!"

"Ok everyone pick a bed!" Janet started walking over to Jacob who picked the bed near Teal'c as Janet wanted to talk to Daniel last.

Janet and Jacks conversation was not all about him leaving or Sam but also about her and her lack of relationships. Janet finished the boy's exams quickly,

"Ok Jacob, Teal'c you are cleared to go Daniel your turn!"

"Thanks Janet!" Daniel whined

Janet looked at him and he knew to shut up straight away something she knew that's why he was left to last. The infirmary was empty as Janet walked over to Daniel's bed with all the gear she needed for his exam.

"Daniel this isn't good, Jack's gone and the impression he gave off he's not coming back. He's given Cassie his Cabin!"

"What his Cabin he would never get rid of it!" Daniel blurted

"He said he can't be around her every day and that he doesn't regret what happen, just that the team got split up. He was sad Daniel; I have never seen him like this. He put on that front you know the one, the big strong Air Force Colonel happy to be going but it was all a front."

"I just can't believe they are doing this to each other!" Janet sighed she had to take Jack's advise and trust him.

"Daniel…am… what are you doing tonight?" Not waiting for his answer.

"Do you want to come over for dinner; Cassie is out so I'm home alone tonight?"

"I can tell you more of what was said!" hoping that get Daniel's interest and he wouldn't decline. She had to do this seeing what has happened with Jack and Sam, Jack was right there is no point in putting it off. She had to know if Daniel felt the same.

Daniel had agreed to have dinner and arranged to be there about 7pm. Daniel headed to the showers while Janet got ready for Sam's exam. While Janet was waiting SG7 came in hot. No one was really badly hurt but Janet was required in surgery so she had missed Sam.

Janet rang Sam later that day to say sorry and to check how she was doing. Sam had said that she was going home and spending some time with her dad and that she would call the next day. Janet was relived that Sam wasn't going to be alone but also that Janet could keep her plans with Daniel.

Janet raced around at five o'clock checking on SG7 and finishing her paper work. She wanted to be home early so she could prepare for tonight. They had organised to order takeout so all she had to do was have a shower chose an outfit and tidy up her room. Just in case it went better than she thought.

As she was having her shower Janet could feel the butterflies building in her stomach, she wasn't this nervous when she got married.

"What if he doesn't feel the same? Oh god what am I doing?" Janet panicked

"Calm down he has feelings just what they are you don't know. If he doesn't feel the same then you will deal with it! You are a Major in the Air Force and a Doctor you can deal with this." Janet told herself.

She finished her shower without any more panic attacks. Choosing an outfit was what took the longest. She chose a pair of denim jeans and an aqua blue shirt. Casual but sexy is what she went for she didn't want to scare the guy away.

Janet looked at her clock, she had ten minutes spare. Pouring a glass of wine for herself, Janet remembered the letter Jack had given her to give to Daniel. She didn't know what was in it but had a fair idea. Going to her draw she grabs it and put it on the dinning room table. As she put the letter down the door bell rang.

Walking to the door, checking that her outfit was right and her hair, doing the final touches as she opened the door. She smiled at the man standing there look drop dead gorgeous in a pair of slacks and a button up shirt. He had been home and showered as well.

"Hi!"

"Hi come on in!" they both were nervous.

"Do you want something to drink?" Janet asked

"Do you have beer?"

"Yeap! I will be back. Am there is a letter from Jack on the table for you, I will get your drink and order dinner while you read it." Janet said as she left the room.

Picking up the letter seeing it was sealed. Label Daniel on the front. He opened it and started to read it.

Dear Daniel,

First I would like to say sorry for breaking up the team and that I haven't got the guts to say goodbye in person. I know you are probably very angry with me at the moment but I have my reasons why. I can't be around her, it hurts too much. It's not her fault I should have been stronger and said no. I basically raped her Daniel now I have to live with the regret. I can't do that there it will kill me seeing her everyday, knowing what I have done. She will be the new CO of SG1 take care of each other. Now I have a few things to say to you and I hope you take this advice.

DON'T WASTE ANY MORE TIME. Make a move, Kiss her, ask her out to dinner, anything tell her how you feel. Don't let your love for Sha'ra get in the way. Sha'ra will always be your wife but she is gone and you deserve to be happy again. Janet is a good person and loves you even if you can't see it. Talk to her. I have told Janet this as well; don't make the mistakes that I have. Don't let her go!

I have a favour to ask, I need you to check in on Sara every now and then. She knows everything about where I am going. She has helped me a lot in the last couple of weeks coming to terms with everything and the move. Thanks!

I will miss you Space monkey. You can come and visit after we settle everything down.

Talk soon your friend.

Jack

Daniel looked straight at Janet who had brought him his beer and got herself another wine. She was looking at him waiting to see his response.

"Is he right? I mean about us, our feelings?" Daniel questioned

"I'm in love with you Daniel! Have been for awhile. I don't know how you feel but I had to tell you that, Jack is right you needed to know that." Before she could say anything else Daniel cupped her face and started a passionate kiss that neither will ever forget.

"I love you too. I can't believe we waste so much time." Daniel stated in between kisses. They talked all night and decided to take it slow.

Daniel gave the letter to Janet to read and they agreed that they needed to get Sam and Jack talking and soon. As soon as Daniel was aloud he would go to the Beta Site and talk to Jack.

A/N Sorry for the delay have been busy with work. Need feedback on what you think. I have decided to go off the Sam and Jack thing for this chapter. I will get to the baby and more at the Beta Site action in the next few chapters.


	8. What do you want

**CHAPTER EIGHT**

Not being able to see Janet for her exam, Sam made some excuses about feeling a little dizzy and if she could get the blood taken tomorrow. The Nurse agreed and let Sam go home early due to the dizziness as long as she had someone with her. Sam organised her Dad and they left the base early. On the way home Sam stoped at a pharmacy and grabbed 2 home pregnancy tests, she needed to know. Sam told her dad that she was getting cramps and wanted some painkillers. Knowing that Jacob would think that it was just that time of month, Sam could get away without too many questions.

"Dad I'm going for a shower, do you want to organise some takeaway, and menus are on the bench in the kitchen." Sam called out as she headed for the bathroom to do the test.

Sam had read the instructions 3 times over to make sure she did everything right.

She followed the instruction to the letter and now all she had to do was wait. Getting undressed to hop into the shower, she was getting excited if she was pregnant she was going to be a mom, then on the other hand if she was pregnant she was probably having Jacks baby which scared her to hell. The timer went off after two minutes; it was her longest two minutes ever. Looking at the stick it had two blue lines on it, grabbing the instructions rereading what the lines meant. Dropping the paper she re looked at the stick, she was pregnant.

"Crap what now?" She asked herself shocked she stepped under the running water and let the tears run down her face. It had been only a couple of hours since she cry over Jack leaving now she was crying again. Not really knowing how she felt, she was relived that she basically knew but she was going to be a mom, she didn't know how to be a mom, she could barely look after herself, and what about Pete, what would he say? What would Jack say and do?

Hopping out of the shower Sam needed advice and the best person for that was down stairs. She didn't know how he will react at her going to become a mother but she needed his support and hoped that is what she got.

"Dad what did you order for dinner?" Sam started

"Am I got chines is that ok?"

"Yeah that's good. How long before it gets here?"

"Should be here any minute!"

"Dad! Can we talk?" Sam jested for Jacob to follow her into the lounge.

Jacob sat down and waited for Sam to start, talking about what had happened was not easy and Sam was eager to talk so he waited.

"Dad I haven't been feeling real well since the beginning of our last mission!" She paused.

"Dad I just did a pregnancy test and it come out positive." Sam spat out as quick as she could.

"What!... No!... What!"

"Dad I think it's the General's baby. Pete and I am haven't you know for a couple of months due to work commitments, and Janet didn't pick anything up when we did that full exams after the virus so that just leaves one conclusion." Sam tried to explain to her dad exactly what she was thinking.

As they sat there trying to process all the information the food arrived so Sam got up and dished out the food, she was hungry now and the chines smelt great. Jacob got up and followed Sam into the kitchen.

"Are you going to keep it? What about Jack and Pete? What are you going to tell them? What about you're Career?" Jacob spat at her.

Not knowing how to answer Sam just sat there thinking.

"Sam talk to me!" Jacob pleaded

Sam sat there some more and thought what was she going to do. She decided that the best thing is to talk it through with Jacob and see what was left at the end.

"Dad, since Jolinar my body hasn't been normal to say the least. Janet and I have discussed it and we didn't think that I would be able to have a child. But now I'm pregnant and I really don't know what to do. Is this my only chance." Taking a breath she came to her decision.

"I can't and won't give this baby up! It's just going to hurt a lot of people and I don't know how to tell them." Sam felt better she had made her mind up. Well truth be told this was the only answer she just had to come to terms with it.

"Oh Sam I am happy for you. I know this is going to be hard and I will try to be there for you as much as I can." Jacob started to think what could she do.

"Sam how much leave have you got stored up?"

"I don't know. Why?" looking puzzled

"You could take some leave and figure what you are going to do about Jack and the baby. Am and you might want to think about Pete and what his reaction is going to be."

"I know dad, Pete wanted kids but I don't really think he is going to want to bring up Jack's baby."

"Sam is Pete who you really wanted any way?" Jacob looking at his daughter hoping she was going to be truthful to herself as well as him.

"Dad I told the General that I regretted that night. And I do regret it. It should never have happened. I was with Pete and I betrayed him. I love Pete dad but I also love Jack, it's just not the same! I could see a life with Pete and I had a life with the General and SG1."

"I was happy with Pete, we did what normal people do. Go to the movies, to dinner, stay at home on the couch. I don't know if I want to give that up. I liked being normal couple." Sam sighed.

"Sam my honest opinion is maybe you don't be with either of them. Maybe it is time for you and your baby. You are strong and smart you can do this. Just be honest with yourself and them."

END OF CHAPTER EIGHT

A/N - I need a Beta reader if anyone is interested. I will try to keep the chapters coming over Christmas. I know it was short sorry I will make the next chapter longer.


	9. Daddy

1The next morning Daniel and Janet said their goodbyes. Daniel was going to con the General to let him go through with Feretti and Janet was going over to Sam's and see how she was doing.

Janet arrived to see Sam packing a bag into her car. Sam said she was going to Marks with her dad. Janet needing to go to the toilet and used Sam's bathroom and noticed the pregnancy test and it all clicked. Janet walked down stairs and asked Jacob to wait out side for her and Sam.

"Sam. How far along are you?" She said as she held up the stick.

"Do you know who the father is?" Janet kept going.

Sam just nodded.

"It's the Colonel's. But no one knows and I don't know what I am going to do yet. I am keeping the baby but I need to sort some things out in my mind before I involve any one else."

Janet took a chance, "You know he thinks he raped you."

"What!" was heard from the door as Jacob was stunned.

Both ladies turned to look at the man standing there.

"You got to be kidding me Jack would never hurt Sam we all know that."

"Daniel is trying to go through with the team today, and talk to him."

"Janet how do you know what he thinks?"

"He wrote a letter to Daniel, he showed me."

"Sam honey I think it is best if you go to Marks, sort out what you want. I'm going to talk to an old friend. Janet, can I get a lift with you to the base?"

"Not a problem Jacob I'm going there now."

"When does the team leave?"

"In about an hour. Daniel is most likely already hounding the General."

Janet, seeing Sam's look of distress, tells her, "Sam don't worry I will talk to Jack, I promise I wont tell him about the baby. You just rest and take care of yourself. I'll talk to you in a couple of days."

"Ok bye Dad, thank you for your support." Sam said sadly while giving her father a big hug. Realizing that she loved to have her dad around and how much she misses her own mother. Now she was going to be one she didn't know what to do. She didn't want her child not knowing his or her father but how was she going to tell him.

Sam headed off to the airport to get her flight as Janet and Jacob got into Janet's car heading into the Base.

"Ok tell me how you lot let this all happen. Tell me that none of you tried to talk some sense into those two. Come on, Daniel can't keep his nose out of anything and Daniel and Teal'c are one of the worse for base gossip. WHAT THE HELL HAPPENED!" Jacob started at Janet.

"Jacob if all you are going to do is yell at me you can get out of the car now, because the last time I checked it was my car and your daughter is a big girl!" Janet yelled back.

Jacob sighed, "I know that Janet, I'm just a normal worried father. You know how it is, you're a parent, it's in our nature to protect them in hard times, and this is one of Sam's."

When they stopped at the red light, Janet looked over and saw the desperation in his eyes, "I know exactly how you feel, but just let her do this one on her own for know. Those two need to work it out, together with nothing else influencing them, especially you."

Jacob sighed again, "Yeah, your right, but can you just tell me what happened?"

Janet then began to tell Jacob the story and she drove them to the base.

A/N I know this is only short I promise the next chapter will be longer.

I have been busy with family and work, I do appoligise to anyone that is

following this story for the delay.


	10. Enjoy your stay Colonel

1 Sam had been at Mark's for a couple of days and was feeling little better. The morning sickness had kept its pace up but as she was just laying around the house she had relaxed a little and that was helping. Sam had come to a couple of decisions and was happy with herself.

Mark had thought he was doing the right thing by calling Pete and telling him about the baby. Mark just naturally thought it was Pete's and didn't ask any questions. All he knew was that Sam was there to relax and recuperate. So when Pete showed up at the house on Friday, Sam was surprised and not ready for the onslaught that hit her.

"Sam I can't believe you! You should have told me! Do you even know who the father is?" Pete yelled as he stood over Sam.

"Pete calm down and we can talk about this."

"I don't want to calm down, we were getting married then you sleep with that scum and now your pregnant! It's his isn't it? I can't believe this. Your going to kept it no matter what aren't you? Aren't You!"

"YES!" Sam yelled standing up so she could look in his face. If she truly was honest it was to protect herself as well. She could fight better standing then having him standing over her while she was stuck on a couch.

"I'm keeping the baby, it is my baby! If you have a problem with it leave!"

Looking at Pete she suddenly made a final decision. In a calm voice Sam said

"Actually Pete I think you should go no matter what. This isn't working and I'm not in love with you. Never have been. This isn't your baby and we both know it. I do care for you but it's not what I want, you're not what I want." With that said Sam left the room passing Mark who had been listening from the door since the yelling started.

"You bitch you just lead me on…"

"Stop right there Pete, I think you should do as Sam asked. I don't agree with what Sam has done but she is my sister and she'll get my full support." Mark said as he jested for the door. Pete followed Mark's instruction and left. But he had left a few nasty phone message on her phone over the next couple of days. Sam had felt better, the morning sickness eased and she had more energy than she can remember in a long time. She had stayed at Mark's for the remainder of the first week then headed back to Colorado to do some damage control.

Sam went into the infirmary to see Janet and tell her everything that had happened with Pete while she was away. Janet was just finishing up with a lady who Sam suspected to be Kerri Johnson the CIA Agent that had gone through to see Jack.

"Hi Janet, just came to see if you are available tonight?"

"I'm sorry Sam, I've already made plans for dinner but that's not till late so we could get together early for a drink." Janet suggested.

"Hi. Sorry Colonel Sam Carter." Sam said as she held out her hand to the woman looking at her.

"Ah, hi. Kerri Johnson, nice to meet the final member of SG1." She said shaking Sam's hand.

"You meet Daniel and Teal'c?"

"Yeah, they came through to the Beta Site with me. Ooh Jacob's your dad right?"

"That's correct. They've all behaved themselves I hope?"

"Most of the time, I think Jacob and Jack had a few words but other than that everyone behaved." Kerri notices the look between the two ladies and just shrugged it off.

"Well sorry to interrupt but Sam I have to finish this and then do some reports for the General, Sam, I'll see you at the normal place say 1700 hours?" Janet said noticing the look Kerri was giving her and Sam.

"Yeah sounds good, I'm not on duty till next week so I'll be there. Do you know if the General is busy today?"

"I have no idea, but the Beta Site debriefing isn't until later today so he might be free now."

"Thanks, bye Janet. Nice to meet you Miss. Johnson, enjoy your stay at the SGC." Sam replied. As she exited the infirmary she heard, "You to Colonel."

Sam headed to General Hammond's office as she approached the door she felt like she was about to lose her morning breakfast. The nerves were starting to get the better of her. She was ready to run in the other direction. It didn't take Sam long to figure she was keeping the baby, it just took longer to accept the decision that she will not be going off world any more and that her dream of commanding her own team will no longer be an option for her. Her dad was right, it was time for her and her unborn child. No matter what happens in there she would be happy.

Sam knocked on the door.

"Enter!"

"Would you have a couple of minutes free Sir?"

"Colonel have a seat. Hope you have enjoyed your down time?"

"Yes Sir I had a relaxing week with Mark and his family."

"What can I do for you?" Seeing that she was having trouble starting what she wanted.

"Sir, I'm… I ….sir I can't take command of SG1 sir."

"Excuse me Colonel?"

"Sir, I am here to request leave of absence from the Air Force."

"Colonel what's going on?"

"Sir, what I am about to tell you is not common knowledge and very personal sir. I… I'm pregnant with General O'Neill's baby sir and no he doesn't know sir."

Too many sir's in there Sam, calm down you aren't standing in front of a firing squad. She commanded herself.

"Colonel, did I just hear you right."

"If you mean that I just told you that I am pregnant and it's the General's, yes sir."

"How long have you known?"

"About a week for sure but a little over two. I kind of figured it out while we were at the Tokra home base."

Hammond sat there for a little while just staring at her, she had the feeling she was under scrutiny.

"I can't let you leave this base Sam." Hammond looked at her with a sad smile.

"What?"

"You do realize that if your pregnancy becomes public knowledge you and your baby will be in danger."

"Sir what are you trying to tell me." Sam was at a total loss what the General was trying to say.

"Sam this baby has your's and Jack's DNA." Seeing Sam still didn't understand.

"You are the smartest person on this base and you haven't figured this out yet. Something defiantly's not right." He chuckled.

"Sam you were a host to a Tokra, you have Naquida in your blood, Jack has the Ancient gene in his. The NID find out about this they will kill you to get this baby."

Sam just sat there stunned. Slumped in the chair, all she could say was, "SHIT!"


End file.
